I used to have a syb3. you really have to cut the last note before you start the next...It is good for your technique
The biggest problem I found was getting the levels, between clean then effect, right through different PAs.

Yep, Johns right, the Boss pedal isn't handling fast passages, the synth effect drops out and you can get some strange squeals and delays. But it is very technique sensitive - you can't play like a usual bass style at all - more like a "triggering" technique. Still, early days, just got it Saturday, and the tones are very good, sounds mental actually.

A compressor first in the chain is meant to improve things but I tried that yesterday and seemed to make it worse by reducing the gaps between notes

Have you tried fiddling with Attack/Release? That might make your synth behave... though it seems only the big, heavy, and expensive (I'm looking at you, Markbass Compressore) have knobs for those two settings.

Had a further long tweak with this beast with a boss compressor in front, quick attack, quick release - its useable with the wet sound low in the overall mix. Would not really recommend it for a pedalboard as its hard to tweak on the fly.
I may treat myself to something for Xmas - haven't seen the EHX on sale in NZ (can you get it here?), but the markbass supersynth seems a reasonable sale price on sale in the states.